The histone deacetylase paralogs HDAC1/2/3 and their corepressor complexes serve as epigenetic master regulators of chromatin function. Over the past decades, HDACs have been widely pursued as pharmacological targets, and considerable efforts have been invested in the development of small molecule drugs. Specifically, ortho-aminoanilide-derived inhibitors, including CI-994 and Cpd-60, stand out with their attractive selectivity profiles and have been used extensively as tools to delineate the biological roles of specific HDAC isoforms and complexes. Here, we apply a suite of activity-independent strategies to investigate how dynamic processes that regulate HDAC complexes govern the isoform and complex selectivity of HDAC inhibitors. Importantly, we find that overreliance on static and simplified biochemical activity assays has confounded the determination of the biological selectivity of these ligands. Our data urge a comprehensive reinterpretation of numerous studies utilizing these tool compounds for the interrogation of epigenetic and other cellular processes.

组蛋白去乙酰化酶旁系同源物 HDAC1/2/3 及其辅阻遏复合物作为染色质功能的表观遗传主调节剂。在过去的几十年里，HDACs 作为药理学靶点被广泛追捧，并且在小分子药物的开发上投入了大量精力。具体来说，邻-氨基苯胺衍生抑制剂，包括 CI-994 和 Cpd-60，以其有吸引力的选择性特征脱颖而出，并已被广泛用作描述特定 HDAC 同工型和复合物的生物学作用的工具。在这里，我们应用一套与活动无关的策略来研究调节 HDAC 复合物的动态过程如何控制 HDAC 抑制剂的异构体和复合物选择性。重要的是，我们发现过度依赖静态和简化的生化活性测定混淆了这些配体的生物选择性的测定。我们的数据敦促对使用这些工具化合物进行表观遗传和其他细胞过程的审讯的众多研究进行全面的重新解释。